Apple has said it plans more explicit consent around granting Mac applications Full Disk Access, particularly as AI agents become more capable. This is a practical reason to review permissions on the Macs that run automation tools, not a reason to abandon those tools.
The current check is straightforward: open macOS Privacy & Security settings, review Full Disk Access and Accessibility permissions, and identify anything you no longer recognize or use. Do not remove permissions from a production service without understanding the impact.
For a development agent, prefer project-folder access over unrestricted home-directory access when possible. Write down any access that must remain enabled for Wake Up or your other services, then make one deliberate change at a time.